XPF_ARATH
ID XPF_ARATH Reviewed; 956 AA.
AC Q9LKI5; Q9SE36; Q9SPL7;
DT 23-NOV-2004, integrated into UniProtKB/Swiss-Prot.
DT 23-NOV-2004, sequence version 2.
DT 03-AUG-2022, entry version 143.
DE RecName: Full=DNA repair endonuclease UVH1;
DE EC=3.1.-.-;
DE AltName: Full=DNA excision repair protein XP-F homolog;
DE AltName: Full=Ultraviolet hypersensitive 1;
DE Short=AtRAD1;
GN Name=UVH1; Synonyms=RAD1; OrderedLocusNames=At5g41150; ORFNames=MEE6.22;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia;
RX PubMed=10758501; DOI=10.1046/j.1365-313x.2000.00694.x;
RA Gallego F., Fleck O., Li A., Wyrzykowska J., Tinland B.;
RT "AtRAD1, a plant homologue of human and yeast nucleotide excision repair
RT endonucleases, is involved in dark repair of UV damages and
RT recombination.";
RL Plant J. 21:507-518(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia;
RX PubMed=10758502; DOI=10.1046/j.1365-313x.2000.00707.x;
RA Liu Z., Hossain G.S., Islas-Osuna M.A., Mitchell D.L., Mount D.W.;
RT "Repair of UV damage in plants by nucleotide excision repair: Arabidopsis
RT UVH1 DNA repair gene is a homolog of Saccharomyces cerevisiae Rad1.";
RL Plant J. 21:519-528(2000).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND MUTAGENESIS OF GLY-756.
RC STRAIN=cv. Landsberg erecta;
RX PubMed=11027708; DOI=10.1104/pp.124.2.579;
RA Fidantsef A.L., Mitchell D.L., Britt A.B.;
RT "The Arabidopsis UVH1 gene is a homolog of the yeast repair endonuclease
RT RAD1.";
RL Plant Physiol. 124:579-586(2000).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9628582; DOI=10.1093/dnares/5.1.41;
RA Sato S., Kaneko T., Kotani H., Nakamura Y., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. IV. Sequence
RT features of the regions of 1,456,315 bp covered by nineteen physically
RT assigned P1 and TAC clones.";
RL DNA Res. 5:41-54(1998).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [7]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 1-688, FUNCTION, AND ALTERNATIVE SPLICING.
RX PubMed=12383497; DOI=10.1016/s0378-1119(02)00869-7;
RA Vonarx E.J., Howlett N.G., Schiestl R.H., Kunz B.A.;
RT "Detection of Arabidopsis thaliana AtRAD1 cDNA variants and assessment of
RT function by expression in a yeast rad1 mutant.";
RL Gene 296:1-9(2002).
RN [8]
RP FUNCTION.
RX PubMed=12393748; DOI=10.1093/embo-reports/kvf211;
RA Dubest S., Gallego M.E., White C.I.;
RT "Role of the AtRad1p endonuclease in homologous recombination in plants.";
RL EMBO Rep. 3:1049-1054(2002).
RN [9]
RP FUNCTION.
RX PubMed=11826311; DOI=10.1105/tpc.010258;
RA Li A., Schuermann D., Gallego F., Kovalchuk I., Tinland B.;
RT "Repair of damaged DNA by Arabidopsis cell extract.";
RL Plant Cell 14:263-273(2002).
RN [10]
RP FUNCTION.
RX PubMed=12554710; DOI=10.1093/jxb/erg069;
RA Hefner E., Preuss S.B., Britt A.B.;
RT "Arabidopsis mutants sensitive to gamma radiation include the homologue of
RT the human repair gene ERCC1.";
RL J. Exp. Bot. 54:669-680(2003).
CC -!- FUNCTION: Seems to be involved in nucleotide excision repair (NER) of
CC damaged DNA (dark repair mechanism). Involved in repair of UV light,
CC and probably oxidative damage. The UVH1/RAD1-ERCC1/RAD10 complex may
CC act as an endonuclease making DNA incision 5' to the lesion site. In
CC vitro, is implicated in double strand breaks (DSBs) repair and is
CC required for homologous recombination in the presence of non-homologous
CC overhangs. May mediate the induction of a DNA-damage sensitive cell-
CC cycle checkpoint during the G2 phase. {ECO:0000269|PubMed:10758501,
CC ECO:0000269|PubMed:10758502, ECO:0000269|PubMed:11027708,
CC ECO:0000269|PubMed:11826311, ECO:0000269|PubMed:12383497,
CC ECO:0000269|PubMed:12393748, ECO:0000269|PubMed:12554710}.
CC -!- SUBUNIT: Heterodimer with ERCC1/RAD10. {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1; Synonyms=AtRAD1-1;
CC IsoId=Q9LKI5-1; Sequence=Displayed;
CC Name=2; Synonyms=AtRAD1-2, AtRAD1-4;
CC IsoId=Q9LKI5-2; Sequence=VSP_011871, VSP_011872;
CC Name=3; Synonyms=AtRAD1-3;
CC IsoId=Q9LKI5-3; Sequence=VSP_011873, VSP_011874;
CC -!- TISSUE SPECIFICITY: Isoform 1 and isoform 2 are widely expressed,
CC predominantly in flowers, meristems and stems. Isoform 3 is detected at
CC low levels. {ECO:0000269|PubMed:10758501, ECO:0000269|PubMed:10758502}.
CC -!- MISCELLANEOUS: [Isoform 2]: Inactive. {ECO:0000305}.
CC -!- MISCELLANEOUS: [Isoform 3]: Inactive. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the XPF family. {ECO:0000305}.
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DR EMBL; AF089003; AAG42948.1; -; mRNA.
DR EMBL; AF160500; AAF01274.1; -; mRNA.
DR EMBL; AF277377; AAF81910.1; -; Genomic_DNA.
DR EMBL; AB010072; BAB09717.1; -; Genomic_DNA.
DR EMBL; CP002688; AED94647.1; -; Genomic_DNA.
DR EMBL; AY140076; AAM98217.1; -; mRNA.
DR EMBL; AF191494; AAF14584.1; -; mRNA.
DR RefSeq; NP_198931.1; NM_123480.4. [Q9LKI5-1]
DR AlphaFoldDB; Q9LKI5; -.
DR SMR; Q9LKI5; -.
DR STRING; 3702.AT5G41150.1; -.
DR PaxDb; Q9LKI5; -.
DR PRIDE; Q9LKI5; -.
DR ProteomicsDB; 242511; -. [Q9LKI5-1]
DR EnsemblPlants; AT5G41150.1; AT5G41150.1; AT5G41150. [Q9LKI5-1]
DR GeneID; 834117; -.
DR Gramene; AT5G41150.1; AT5G41150.1; AT5G41150. [Q9LKI5-1]
DR KEGG; ath:AT5G41150; -.
DR Araport; AT5G41150; -.
DR TAIR; locus:2163011; AT5G41150.
DR eggNOG; KOG0442; Eukaryota.
DR HOGENOM; CLU_002265_2_0_1; -.
DR InParanoid; Q9LKI5; -.
DR OMA; FHKILQA; -.
DR PhylomeDB; Q9LKI5; -.
DR PRO; PR:Q9LKI5; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9LKI5; baseline and differential.
DR Genevisible; Q9LKI5; AT.
DR GO; GO:0000110; C:nucleotide-excision repair factor 1 complex; IBA:GO_Central.
DR GO; GO:0003684; F:damaged DNA binding; IBA:GO_Central.
DR GO; GO:0003697; F:single-stranded DNA binding; IBA:GO_Central.
DR GO; GO:0000014; F:single-stranded DNA endodeoxyribonuclease activity; IMP:TAIR.
DR GO; GO:0006281; P:DNA repair; IEP:TAIR.
DR GO; GO:0000724; P:double-strand break repair via homologous recombination; IMP:TAIR.
DR GO; GO:0006289; P:nucleotide-excision repair; IMP:TAIR.
DR GO; GO:1901255; P:nucleotide-excision repair involved in interstrand cross-link repair; IBA:GO_Central.
DR GO; GO:0006296; P:nucleotide-excision repair, DNA incision, 5'-to lesion; IBA:GO_Central.
DR GO; GO:0000720; P:pyrimidine dimer repair by nucleotide-excision repair; IMP:CACAO.
DR GO; GO:0000712; P:resolution of meiotic recombination intermediates; IBA:GO_Central.
DR GO; GO:0006979; P:response to oxidative stress; IMP:TAIR.
DR GO; GO:0009314; P:response to radiation; IEP:TAIR.
DR InterPro; IPR006166; ERCC4_domain.
DR InterPro; IPR011335; Restrct_endonuc-II-like.
DR InterPro; IPR010994; RuvA_2-like.
DR Pfam; PF02732; ERCC4; 1.
DR SMART; SM00891; ERCC4; 1.
DR SUPFAM; SSF47781; SSF47781; 1.
DR SUPFAM; SSF52980; SSF52980; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; DNA damage; DNA excision; DNA recombination;
KW DNA repair; DNA-binding; Endonuclease; Hydrolase; Nuclease; Nucleus;
KW Reference proteome.
FT CHAIN 1..956
FT /note="DNA repair endonuclease UVH1"
FT /id="PRO_0000198862"
FT DOMAIN 725..805
FT /note="ERCC4"
FT REGION 343..363
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 516..593
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 697..718
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 256..272
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255"
FT COMPBIAS 516..530
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 532..550
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 551..565
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 697..713
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 689..727
FT /note="DGLCMGSNSSTEFPASSTQNSLTRKAGGRKELEKETQVI -> FLFPAFFSS
FT ILCYKLGIRMGSAWGRILLQSFQLGVHKTH (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_011871"
FT VAR_SEQ 728..956
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_011872"
FT VAR_SEQ 781..783
FT /note="GRL -> VFE (in isoform 3)"
FT /evidence="ECO:0000305"
FT /id="VSP_011873"
FT VAR_SEQ 784..956
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000305"
FT /id="VSP_011874"
FT MUTAGEN 756
FT /note="G->D: Loss of DNA repair activity."
FT /evidence="ECO:0000269|PubMed:11027708"
FT CONFLICT 22
FT /note="L -> V (in Ref. 3; AAF81910)"
FT /evidence="ECO:0000305"
FT CONFLICT 117
FT /note="S -> A (in Ref. 3; AAF81910)"
FT /evidence="ECO:0000305"
FT CONFLICT 147
FT /note="S -> G (in Ref. 3; AAF81910)"
FT /evidence="ECO:0000305"
FT CONFLICT 434
FT /note="D -> G (in Ref. 7; AAF14584)"
FT /evidence="ECO:0000305"
FT CONFLICT 544
FT /note="P -> L (in Ref. 3; AAF81910)"
FT /evidence="ECO:0000305"
FT CONFLICT 548
FT /note="R -> Q (in Ref. 3; AAF81910)"
FT /evidence="ECO:0000305"
FT CONFLICT 559
FT /note="T -> A (in Ref. 3; AAF81910)"
FT /evidence="ECO:0000305"
FT CONFLICT 720
FT /note="L -> V (in Ref. 3; AAF81910)"
FT /evidence="ECO:0000305"
FT CONFLICT 837
FT /note="F -> S (in Ref. 3; AAF81910)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 956 AA; 107635 MW; B766CF7522521610 CRC64;
MALKYHQQII SDLLEDSNGG LLILSSGLSL AKLIASLLIL HSPSQGTLLL LLSPAAQSLK
SRIIHYISSL DSPTPTEITA DLPANQRYSL YTSGSPFFIT PRILIVDLLT QRIPVSSLAG
IFILNAHSIS ETSTEAFIIR IVKSLNSSAY IRAFSDRPQA MVSGFAKTER TMRALFLRKI
HLWPRFQLDV SQELEREPPE VVDIRVSMSN YMVGIQKAII EVMDACLKEM KKTNKVDVDD
LTVESGLFKS FDEIVRRQLD PIWHTLGKRT KQLVSDLKTL RKLLDYLVRY DAVSFLKFLD
TLRVSESYRS VWLFAESSYK IFDFAKKRVY RLVKASDVKS KEHVKNKSGK KRNSKGETDS
VEAVGGETAT NVATGVVVEE VLEEAPKWKV LREILEETQE ERLKQAFSEE DNSDNNGIVL
VACKDERSCM QLEDCITNNP QKVMREEWEM YLLSKIELRS MQTPQKKKQK TPKGFGILDG
VVPVTTIQNS EGSSVGRQEH EALMAAASSI RKLGKTTDMA SGNNNPEPHV DKASCTKGKA
KKDPTSLRRS LRSCNKKTTN SKPEILPGPE NEEKANEAST SAPQEANAVR PSGAKKLPPV
HFYALESDQP ILDILKPSVI IVYHPDMGFV RELEVYKAEN PLRKLKVYFI FYDESTEVQK
FEASIRRENE AFESLIRQKS SMIIPVDQDG LCMGSNSSTE FPASSTQNSL TRKAGGRKEL
EKETQVIVDM REFMSSLPNV LHQKGMKIIP VTLEVGDYIL SPSICVERKS IQDLFQSFTS
GRLFHQVEMM SRYYRIPVLL IEFSQDKSFS FQSSSDISDD VTPYNIISKL SLLVLHFPRL
RLLWSRSLHA TAEIFTTLKS NQDEPDETRA IRVGVPSEEG IIENDIRAEN YNTSAVEFLR
RLPGVSDANY RSIMEKCKSL AELASLPVET LAELMGGHKV AKSLREFLDA KYPTLL
